UFC officials announced the bout on Saturday. The event will take place inside Sprint Center.
Waterson (14-4) is coming off a resounding first-round submission win over Paige VanZant in December. Fighting out of Jackson-Wink MMA in Albuquerque, New Mexico, Waterson has been limited to just two appearances in the UFC since signing with the promotion in 2015, but she finished both opponents she has faced.
The 31-year-old is a former atomweight champion in all-female promotion Invicta FC.
Namajunas (5-3) will enter the contest off a split decision loss to Karolina Kowalkiewicz at UFC 201 last July. The Denver-based strawweight fought Carla Esparza for the inaugural 115-pound title in December 2014. She is 3-2 overall in the UFC.
ESPN.com ranks Namajunas and Waterson the Nos. 6 and 8 strawweights in the world, respectively.